Version update from 10.1.600 to 10.2.400 blank out settings?

We recently updated our Development database from 10.1.600.35 to 10.2.400.14.
During our testing we discovered settings in the user accounts and settings for AP Electronic Payments disappearing.
I did a similar test going from 10.1.600.35 to 10.2.500.3 and had similar results.
Has anyone else noticed any settings/setup missing after their update?

Chris Wineinger
Dorner Mfg